Colonel Richard McKeon, the superintendent of the State Police, announced he is retiring next week amid disclosures that he ordered a state trooper to remove embarrassing information from an arrest report about the daughter of a judge. He also punished the trooper for including the information in his report.

“I have today decided that putting the greater good of the Massachusetts state police first necessitates my decision to retire after 35 years of proud service,” wrote McKeon, 61, in an e-mail to 2,200 state troopers late on Friday afternoon.

McKeon had drawn widespread criticism for ordering Trooper Ryan Sceviour to alter the report he wrote after arresting Alli Bibaud in Worcester on charges of drunken driving and driving under the influence of drugs on Oct. 16. Her father, Timothy Bibaud, is the first justice of Dudley District Court and presides over the drug court there.

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Sceviour this week filed a federal lawsuit against McKeon, alleging he was reprimanded and forced to falsify official records to protect the judge’s daughter. He said he was ordered to remove Alli Bibaud’s admission that she has traded sex for heroin as well as her rant that her father was a judge who would be furious about her arrest.

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McKeon suggested that he was just trying to treat a victim of opioid addiction with sensitivity and respect. He also said he has told troopers “more times than I can remember” to focus their reports only on the charges against the individual.

“In our law enforcement role, our first duty is to enforce the law and protect the public, but that doesn’t preclude us from being empathetic toward those in need,” he wrote in a separate resignation letter to Public Safety Secretary Daniel Bennett.

McKeon, chosen by Governor Charlie Baker to lead the State Police in July 2015, had been in charge of the State Police detectives assigned to the Worcester DA’s office for several years.

At the time, Worcester District Attorney Joseph D. Early Jr. called McKeon “one of the most intelligent people I’ve ever met, but at the same time, one of the most humble.”

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Baker, who on Thursday said he would quickly investigate the “significant set of serious allegations” made by Sceviour, on Friday thanked McKeon for his service.

“The Governor believes that Colonel McKeon made a mistake by getting involved in the Bibaud case and has ordered the State Police to examine procedures for the review of arrest reports,” wrote communications director Lizzy Guyton.

“Governor Baker recognizes the motivation to protect those with substance use disorders from potentially embarrassing information contained in their public records,” Guyton added. Nonetheless, the governor “expects the courts to hold the defendant accountable for all charges stemming from this incident.”

A spokeswoman for Attorney General Maura Healey said her office would continue investigating Bibaud’s altered arrest report.

“The allegations at issue here are very serious,” said the spokeswoman, Jillian Fennimore, in a statement.

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Also on Friday, state officials said they would invalidate reprimands given by State Police officials to Sceviour and Jason Conant, the sergeant who approved his report.

Dana Pullman, president of the State Police Association of Massachusetts, called McKeon’s retirement “a good start to rectify the misuse of power that took place under his administration.”

But, he added: “It’s imperative that the new colonel make sweeping changes at all levels of the command staff and leadership to fully address this matter. We need stop the blatant abuse of power.”

Lenny Kesten, the lawyer who filed suit on behalf of Sceviour, said: “It’s unfortunate that the colonel’s career has to end under this cloud. However, he is responsible for ordering state troopers to alter police reports and shred logs.”

Bibaud, 30, crashed her car on Interstate 190 in Worcester on Oct. 16. When Sceviour arrived, she reeked of alcohol and had what he described as a “heroin kit,” including a dozen needles and a spoon, according to his police report. She admitted performing sex acts on men to support her addiction, according to his original report, and offered sex to the trooper in return for leniency.

Then Bibaud cried and screamed that her father was a judge. “He’s going to kill me,” she screamed, according to the report.

She was charged with operating under the influence of alcohol, operating under the influence of narcotics, negligent operation of a motor vehicle, a marked lanes violation, and failure to have a valid inspection sticker.

She was released and picked up by her father. She was admitted to a rehab facility, according to court records.

Two days later, a trooper came to Sceviour’s house on his day off to summon him to the State Police barracks in Holden — 90 miles away.

There, Sceviour and Conant were given negative “supervisory observation reports” to reprimand them for including statements made by Bibaud about sex as well as her father.

Judge Bibaud has said he did not ask for changes in his daughter’s arrest report, and has said he believes she needs help with her addiction.

Sceviour was instructed to bring the edited report to Worcester District Court — to swap for the original report in the court file, according to the lawsuit Sceviour filed earlier this week in US District Court in Boston. But officials scrapped the plan, the suit alleges, when they realized it would probably be discovered.

Instead, a top aide to Worcester District Attorney Early made an oral motion to redact the police report, which was allowed by the presiding judge.

Judge Bibaud, as well as McKeon and the state public safety secretary, Daniel Bennett, all worked in the Worcester district attorney’s office.

As an investigator for the district attorney, McKeon was assigned to many high-profile cases, including the abduction of 16-year-old Warren lifeguard Molly Bish; the murder of Paxton Police Chief Robert J. Mortell; and the disappearance of Kevin Harkins, who was last seen in a Worcester bar in 1994 and was declared dead in 2008, Early’s office said.

McKeon’s retirement will take effect on Nov. 17, and his successor is expected to be named shortly, officials said.